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lumpy: drop

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Removed because it requires python2 and the upstream repository looks
undermaintained.
This commit is contained in:
Martin Weinelt 2022-01-12 02:33:33 +01:00
parent 369db3b2f3
commit 492e5e07c9
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GPG key ID: 87C1E9888F856759
3 changed files with 1 additions and 52 deletions
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50
pkgs/applications/science/biology/lumpy/default.nix
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@ -1,50 +0,0 @@
{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
, samtools, hexdump, python2Packages, which }:
let
python =
python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
in stdenv.mkDerivation rec {
pname = "lumpy";
version = "0.3.1";
src = fetchFromGitHub {
owner = "arq5x";
repo = "lumpy-sv";
rev = "v${version}";
sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
fetchSubmodules = true;
};
nativeBuildInputs = [ which ];
buildInputs =
[ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
preConfigure = ''
patchShebangs ./.
# Use Nix htslib over bundled version
sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
# Also make sure we use the includes from Nix's htslib
sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
'';
# Upstream's makefile doesn't have an install target
installPhase = ''
mkdir -p $out
cp -r bin $out
cp -r scripts $out
sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
'';
meta = with lib; {
description = "Probabilistic structural variant caller";
homepage = "https://github.com/arq5x/lumpy-sv";
maintainers = with maintainers; [ jbedo ];
license = licenses.mit;
platforms = [ "x86_64-linux" ];
};
}

1
pkgs/top-level/aliases.nix
View file

@ -568,6 +568,7 @@ mapAliases ({
lua5_1_sockets = lua51Packages.luasocket; # added 2017-05-02
lua5_expat = luaPackages.luaexpat; # added 2017-05-02
lua5_sec = luaPackages.luasec; # added 2017-05-02
lumpy = throw "lumpy has been removed from nixpkgs, as it is stuck on python2."; # added 2022-01-12
lxappearance-gtk3 = throw "lxappearance-gtk3 has been removed. Use lxappearance instead, which now defaults to Gtk3"; # added 2020-06-03
lzma = xz; # moved from top-level 2021-03-14
m3d-linux = m33-linux; # added 2016-08-13

2
pkgs/top-level/all-packages.nix
View file

@ -31669,8 +31669,6 @@ with pkgs;
last = callPackage ../applications/science/biology/last { };
lumpy = callPackage ../applications/science/biology/lumpy { };
macse = callPackage ../applications/science/biology/macse { };
MACS2 = callPackage ../applications/science/biology/MACS2 { };